Mike Phelps sent this tip around to our team a couple weeks ago. I've experienced this problem and never put all the pieces before. Not it makes perfect sense. Now if I coule get him to start his own blog ;)
IIS runs strictly from memory (i.e, the IIS metabase is loaded to RAM). If you make changes to IIS, they are only made in memory. The changes don't actually stick until IIS writes to disk. This can occur with safely shutting down windows, or restarting IIS without a timeout/clicking End Now.
Want to see for yourself?
1) Go to properties of the DataPortal web site, and change the anonymous credentials to be your user.
2) Close the IIS control panel.
3) Start/Run iisreset /timeout:0
A)This forces IIS to shut down, without saving to disk. The wait time is used to persist to disk.
4) Check the user you changed in #1. It will be back to the original user.
The point: Be wary of using the timeout option when you've made metabase changes.